Accessing 1000G/Hapmap Data

Question

[Gabriel R.]

I never looked at 1000g/hapmap/complete genomics data before, I seek to have access to the aligned genomic data (bam format)for the following three individuals:

1. NA20356
2. NA20357
3. NA20358

which are together in this file: http://hapmap.ncbi.nlm.nih.gov/downloads/samples_individuals/relationships_w_pops_121708.txt

If you choose to answer this question :

1. Yes I know about the hapmap and 1000g ftp sites, I searched a lot on them but to no avail hence biostars.
2. Yes I googled it
3. Please provide links for all 3.

Thanks !

Answer 1

[Bert Overduin]

A list of current alignment files for the 1000 Genomes Project can be found in the alignment index:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment.index

The files you are looking for can be found here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20356/

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20357/

Also please read:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.alignment_data

[Gabriel R.]

Copy paste error, I corrected my post, where is NA20358 ?

[Bert Overduin]

Looks like that individual hasn't been sequenced yet (or at least we don't have the data yet), but I am currently trying to find out.

[Bert Overduin]

I can now confirm that NA20358 hasn't been sequenced and afaik won't be either.

[Laura]

We do have omni, axiom and the illumina lof exome chip data on this individual though

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120131_omni_genotypes_and_intensities/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110210_Affymetrix_Axiom/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20121009_broad_exome_chip/